+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
-
-import org.junit.Test;
-
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
+import jalview.util.MapList;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import org.junit.Test;
public class AlignmentUtilsTests
{
+ // @formatter:off
+ private static final String TEST_DATA =
+ "# STOCKHOLM 1.0\n" +
+ "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
+ "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
+ "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
+ "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
+ "#=GR D.melanogaster.1 SS ................((((\n" +
+ "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
+ "#=GR D.melanogaster.2 SS ................((((\n" +
+ "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
+ "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
+ "//";
+
+ private static final String AA_SEQS_1 =
+ ">Seq1Name\n" +
+ "K-QY--L\n" +
+ ">Seq2Name\n" +
+ "-R-FP-W-\n";
+
+ private static final String CDNA_SEQS_1 =
+ ">Seq1Name\n" +
+ "AC-GG--CUC-CAA-CT\n" +
+ ">Seq2Name\n" +
+ "-CG-TTA--ACG---AAGT\n";
+
+ private static final String CDNA_SEQS_2 =
+ ">Seq1Name\n" +
+ "GCTCGUCGTACT\n" +
+ ">Seq2Name\n" +
+ "GGGTCAGGCAGT\n";
+ // @formatter:on
+
public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
+
@Test
public void testExpandFlanks()
{
assertTrue("Flanking sequence not the same as original dataset sequence.\n"+ung+"\n"+sq.getDatasetSequence().getSequenceAsString(),ung.equalsIgnoreCase(sq.getDatasetSequence().getSequenceAsString()));
}
}
+ }
}
+
+ /**
+ * Test method that returns a map of lists of sequences by sequence name.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testGetSequencesByName() throws IOException
+ {
+ final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
+ + ">Seq1Name\nABCD\n";
+ AlignmentI al = loadAlignment(data, "FASTA");
+ Map<String, List<SequenceI>> map = AlignmentUtils
+ .getSequencesByName(al);
+ assertEquals(2, map.keySet().size());
+ assertEquals(2, map.get("Seq1Name").size());
+ assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
+ assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
+ assertEquals(1, map.get("Seq2Name").size());
+ assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
+ }
+ /**
+ * Helper method to load an alignment and ensure dataset sequences are set up.
+ *
+ * @param data
+ * @param format TODO
+ * @return
+ * @throws IOException
+ */
+ protected AlignmentI loadAlignment(final String data, String format) throws IOException
+ {
+ Alignment a = new FormatAdapter().readFile(data,
+ AppletFormatAdapter.PASTE, format);
+ a.setDataset(null);
+ return a;
+ }
+ /**
+ * Test mapping of protein to cDNA.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapProteinToCdna() throws IOException
+ {
+ // protein: Human + Mouse, 3 residues
+ AlignmentI protein = loadAlignment(
+ ">Human\nKQY\n>Mouse\nAFP\n>Worm\nRST\n",
+ "FASTA");
+ // cDNA: Mouse, Human, Mouse, 9 bases
+ // @formatter:off
+ String dnaData =
+ ">Mouse\nGAAATCCAG\n" +
+ ">Human\nTTCGATTAC\n" +
+ ">Mouse\nGTCGTTTGC\n" +
+ ">Mouse\nGTCGTTTGCgac\n" + // not mapped - wrong length
+ ">Fly\nGTCGTTTGC\n"; // not mapped - no name match
+ // @formatter:on
+ AlignmentI cdna1 = loadAlignment(
+ dnaData,
+ "FASTA");
+ boolean mapped = AlignmentUtils.mapProteinToCdna(protein, cdna1);
+ assertTrue(mapped);
+
+ /*
+ * Check two mappings (one for Mouse, one for Human)
+ */
+ assertEquals(2, protein.getCodonFrames().length);
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).length);
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).length);
+
+ /*
+ * Inspect mapping for Human protein
+ */
+ AlignedCodonFrame humanMapping = protein.getCodonFrame(protein
+ .getSequenceAt(0))[0];
+ assertEquals(1, humanMapping.getdnaSeqs().length);
+ assertEquals(cdna1.getSequenceAt(1).getDatasetSequence(),
+ humanMapping.getdnaSeqs()[0]);
+ Mapping[] protMappings = humanMapping.getProtMappings();
+ assertEquals(1, protMappings.length);
+ MapList mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges()));
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges()));
+
+ /*
+ * Inspect mappings for Mouse protein
+ */
+ AlignedCodonFrame mouseMapping1 = protein.getCodonFrame(protein
+ .getSequenceAt(1))[0];
+ assertEquals(2, mouseMapping1.getdnaSeqs().length);
+ assertEquals(cdna1.getSequenceAt(0).getDatasetSequence(),
+ mouseMapping1.getdnaSeqs()[0]);
+ assertEquals(cdna1.getSequenceAt(2).getDatasetSequence(),
+ mouseMapping1.getdnaSeqs()[1]);
+ protMappings = mouseMapping1.getProtMappings();
+ assertEquals(2, protMappings.length);
+ for (int i = 0; i < 2; i++)
+ {
+ mapList = protMappings[i].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges()));
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges()));
+ }
+ }
+
+ /**
+ * Test mapping of protein to cDNA which may include start and/or stop codons.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapProteinToCdna_stopStartCodons() throws IOException
+ {
+ // protein: Human + Mouse, 3 residues
+ AlignmentI protein = loadAlignment(
+ ">Human\nKQY\n>Mouse\nAFP\n>Worm\nRST\n", "FASTA");
+ // @formatter:off
+ String dnaData =
+ ">Mouse\natgGAAATCCAG\n" + // Mouse with start codon
+ ">Human\nTTCGATtactaa\n" + // Human with stop codon TAA
+ ">Mouse\nGTCGTTTGctaG\n" + // Mouse with stop codon TAG
+ ">Human\nGTCGTTTgctGa\n" + // Human with stop codon TGA
+ ">Mouse\nATGGTCGTTTGCtag\n"; // Mouse with start and stop codons
+ // @formatter:on
+ AlignmentI cdna1 = loadAlignment(
+ dnaData,
+ "FASTA");
+ boolean mapped = AlignmentUtils.mapProteinToCdna(protein, cdna1);
+ assertTrue(mapped);
+
+ /*
+ * Check two mappings (one for Mouse, one for Human)
+ */
+ assertEquals(2, protein.getCodonFrames().length);
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).length);
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).length);
+
+ /*
+ * Inspect mapping for Human protein - should map to 2nd and 4th cDNA seqs
+ */
+ AlignedCodonFrame humanMapping = protein.getCodonFrame(protein
+ .getSequenceAt(0))[0];
+ assertEquals(2, humanMapping.getdnaSeqs().length);
+ assertEquals(cdna1.getSequenceAt(1).getDatasetSequence(),
+ humanMapping.getdnaSeqs()[0]);
+ assertEquals(cdna1.getSequenceAt(3).getDatasetSequence(),
+ humanMapping.getdnaSeqs()[1]);
+ Mapping[] protMappings = humanMapping.getProtMappings();
+ // two mappings, both to cDNA with stop codon
+ assertEquals(2, protMappings.length);
+ MapList mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges()));
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges()));
+ mapList = protMappings[1].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges()));
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges()));
+
+ /*
+ * Inspect mapping for Mouse protein - should map to 1st/3rd/5th cDNA seqs
+ */
+ AlignedCodonFrame mouseMapping = protein.getCodonFrame(protein
+ .getSequenceAt(1))[0];
+ assertEquals(3, mouseMapping.getdnaSeqs().length);
+ assertEquals(cdna1.getSequenceAt(0).getDatasetSequence(),
+ mouseMapping.getdnaSeqs()[0]);
+ assertEquals(cdna1.getSequenceAt(2).getDatasetSequence(),
+ mouseMapping.getdnaSeqs()[1]);
+ assertEquals(cdna1.getSequenceAt(4).getDatasetSequence(),
+ mouseMapping.getdnaSeqs()[2]);
+
+ // three mappings
+ protMappings = mouseMapping.getProtMappings();
+ assertEquals(3, protMappings.length);
+
+ // first mapping to cDNA with start codon
+ mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges()));
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges()));
+
+ // second mapping to cDNA with stop codon
+ mapList = protMappings[1].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges()));
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges()));
+
+ // third mapping to cDNA with start and stop codon
+ mapList = protMappings[2].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ assertTrue(Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges()));
+ assertTrue(Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges()));
}
}
git://source.jalview.org / jalview.git / blobdiff